Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_002721134.1 RSPH17029_RS12960 TRAP transporter substrate-binding protein
Query= SwissProt::P37735 (333 letters) >NCBI__GCF_000015985.1:WP_002721134.1 Length = 334 Score = 584 bits (1505), Expect = e-171 Identities = 293/331 (88%), Positives = 309/331 (93%) Query: 1 MLTRRILGALVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNG 60 MLTRR L AL GA AL+LA +VPALA+PIVIKFSHVVAPDTPKGKGA KFEELAEKYT+G Sbjct: 1 MLTRRSLAALAGAAALALAAAVPALAQPIVIKFSHVVAPDTPKGKGATKFEELAEKYTDG 60 Query: 61 AVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEAL 120 AVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFK Y+AL Sbjct: 61 AVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKGYDAL 120 Query: 121 HKVTQGEAGKMLLSKLEAKGITGLAFWDNGFKIMSANTPLTMPDDFLGLKMRIQSSKVLE 180 H VT GE GKML SKLE KGI GLA+WDNGFKIMSAN+P+ PDDFLGLKMRIQSSKVLE Sbjct: 121 HTVTNGEVGKMLFSKLEDKGIKGLAYWDNGFKIMSANSPIATPDDFLGLKMRIQSSKVLE 180 Query: 181 AEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYA 240 A+MNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNM+TQKM+EVQKHATVSNHGYLGYA Sbjct: 181 AQMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMYTQKMHEVQKHATVSNHGYLGYA 240 Query: 241 VIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEE 300 VIVNKQFWDGLP +VR GLEKA+ E+TDYANGIAKEEN+KALQAMKDAGTTEFHELT EE Sbjct: 241 VIVNKQFWDGLPEEVRAGLEKALTEATDYANGIAKEENDKALQAMKDAGTTEFHELTPEE 300 Query: 301 RAAWEEVLTPVHDEMAERIGAETIAAVKAAT 331 AAWEEVL PVH+EMA RIGAETIAAVKAAT Sbjct: 301 LAAWEEVLAPVHEEMAGRIGAETIAAVKAAT 331 Lambda K H 0.314 0.130 0.364 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 467 Number of extensions: 8 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 333 Length of database: 334 Length adjustment: 28 Effective length of query: 305 Effective length of database: 306 Effective search space: 93330 Effective search space used: 93330 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory